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  <div class="section" id="module-pysimm.lmps">
<span id="pysimm-lmps-module"></span><h1>pysimm.lmps module<a class="headerlink" href="#module-pysimm.lmps" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pysimm.lmps.CreateBox">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">CreateBox</code><span class="sig-paren">(</span><em>n=1</em>, <em>region=&lt;pysimm.lmps.Region object&gt;</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#CreateBox"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.CreateBox" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pysimm.utils.html#pysimm.utils.Item" title="pysimm.utils.Item"><code class="xref py py-class docutils literal"><span class="pre">pysimm.utils.Item</span></code></a></p>
<p>Template object to create a box in a LAMMPS simulation. See LAMMPS documentation for further information</p>
<dl class="attribute">
<dt id="pysimm.lmps.CreateBox.n">
<code class="descname">n</code><a class="headerlink" href="#pysimm.lmps.CreateBox.n" title="Permalink to this definition">¶</a></dt>
<dd><p>number of atom types</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.CreateBox.region">
<code class="descname">region</code><a class="headerlink" href="#pysimm.lmps.CreateBox.region" title="Permalink to this definition">¶</a></dt>
<dd><p><a class="reference internal" href="#pysimm.lmps.Region" title="pysimm.lmps.Region"><code class="xref py py-class docutils literal"><span class="pre">Region</span></code></a> object</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">**kwargs</code></dt>
<dd><p>optional kwargs for create_box command (replace / with _)</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.CreateBox.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#CreateBox.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.CreateBox.write" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.CustomInput">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">CustomInput</code><span class="sig-paren">(</span><em>custom_input</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#CustomInput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.CustomInput" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Template object to contain custom LAMMPS input.</p>
<dl class="attribute">
<dt id="pysimm.lmps.CustomInput.custom_input">
<code class="descname">custom_input</code><a class="headerlink" href="#pysimm.lmps.CustomInput.custom_input" title="Permalink to this definition">¶</a></dt>
<dd><p>custom input string</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.CustomInput.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#CustomInput.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.CustomInput.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Create LAMMPS input for a custom simulation.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; pysimm.lmps.Simulation object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">input string</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Group">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Group</code><span class="sig-paren">(</span><em>name='all'</em>, <em>style='id'</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Group"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Group" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pysimm.utils.html#pysimm.utils.Item" title="pysimm.utils.Item"><code class="xref py py-class docutils literal"><span class="pre">pysimm.utils.Item</span></code></a></p>
<p>Template object to define a group in a LAMMPS simulation. See LAMMPS documentation for further information</p>
<dl class="attribute">
<dt id="pysimm.lmps.Group.name">
<code class="descname">name</code><a class="headerlink" href="#pysimm.lmps.Group.name" title="Permalink to this definition">¶</a></dt>
<dd><p>name for the group</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Group.style">
<code class="descname">style</code><a class="headerlink" href="#pysimm.lmps.Group.style" title="Permalink to this definition">¶</a></dt>
<dd><p>style for the group</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">*args</code></dt>
<dd><p>arguments for the given style</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Group.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Group.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Group.write" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Init">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Init</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Init"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Init" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Template object to contain LAMMPS initialization settings</p>
<dl class="attribute">
<dt id="pysimm.lmps.Init.forcefield">
<code class="descname">forcefield</code><a class="headerlink" href="#pysimm.lmps.Init.forcefield" title="Permalink to this definition">¶</a></dt>
<dd><p>name of a supported force field; simulation settings will be chosen based on the force field name</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.units">
<code class="descname">units</code><a class="headerlink" href="#pysimm.lmps.Init.units" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS set of units to use during simulation; default=real</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.atom_style">
<code class="descname">atom_style</code><a class="headerlink" href="#pysimm.lmps.Init.atom_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS aomt_style to use during simulation; default=full</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.charge">
<code class="descname">charge</code><a class="headerlink" href="#pysimm.lmps.Init.charge" title="Permalink to this definition">¶</a></dt>
<dd><p>option to define if any particles in system a non-zero charge</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.kspace_style">
<code class="descname">kspace_style</code><a class="headerlink" href="#pysimm.lmps.Init.kspace_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS kspace_style to use during simulation if system has charges; default=pppm 1e-4</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.cutoff">
<code class="descname">cutoff</code><a class="headerlink" href="#pysimm.lmps.Init.cutoff" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of cutoff distances for nonbonded interactions; default={&#8216;lj&#8217;: 12.0, &#8216;coul&#8217;: 12.0, &#8216;inner_lj&#8217;: 10.0}</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.pair_style">
<code class="descname">pair_style</code><a class="headerlink" href="#pysimm.lmps.Init.pair_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS pair_style to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.bond_style">
<code class="descname">bond_style</code><a class="headerlink" href="#pysimm.lmps.Init.bond_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS bond_style to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.angle_style">
<code class="descname">angle_style</code><a class="headerlink" href="#pysimm.lmps.Init.angle_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS angle_style to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.dihedral_style">
<code class="descname">dihedral_style</code><a class="headerlink" href="#pysimm.lmps.Init.dihedral_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS dihedral_style to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.improper_style">
<code class="descname">improper_style</code><a class="headerlink" href="#pysimm.lmps.Init.improper_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS improper_style to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.special_bonds">
<code class="descname">special_bonds</code><a class="headerlink" href="#pysimm.lmps.Init.special_bonds" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS special_bonds to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.pair_modify">
<code class="descname">pair_modify</code><a class="headerlink" href="#pysimm.lmps.Init.pair_modify" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS pair_modify to use during simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Init.read_data">
<code class="descname">read_data</code><a class="headerlink" href="#pysimm.lmps.Init.read_data" title="Permalink to this definition">¶</a></dt>
<dd><p>name of data file to read instead of using <a class="reference internal" href="pysimm.system.html#pysimm.system.System" title="pysimm.system.System"><code class="xref py py-class docutils literal"><span class="pre">System</span></code></a> object</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Init.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Init.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Init.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Prepare LAMMPS input with initialization settings</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Simulation" title="pysimm.lmps.Simulation"><code class="xref py py-class docutils literal"><span class="pre">Simulation</span></code></a> object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">string of LAMMPS input</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.LogFile">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">LogFile</code><span class="sig-paren">(</span><em>fname</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#LogFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.LogFile" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Class to read LAMMPS log file into Pandas DataFrame stored in LogFile.data</p>
<dl class="attribute">
<dt id="pysimm.lmps.LogFile.fname">
<code class="descname">fname</code><a class="headerlink" href="#pysimm.lmps.LogFile.fname" title="Permalink to this definition">¶</a></dt>
<dd><p>filename of log file</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.LogFile.data">
<code class="descname">data</code><a class="headerlink" href="#pysimm.lmps.LogFile.data" title="Permalink to this definition">¶</a></dt>
<dd><p>resulting DataFrame with log file data</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Minimization">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Minimization</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Minimization"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Minimization" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Template object to contain LAMMPS energy minimization settings.</p>
<dl class="attribute">
<dt id="pysimm.lmps.Minimization.min_style">
<code class="descname">min_style</code><a class="headerlink" href="#pysimm.lmps.Minimization.min_style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS minimization style default=&#8217;sd&#8217;</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Minimization.dmax">
<code class="descname">dmax</code><a class="headerlink" href="#pysimm.lmps.Minimization.dmax" title="Permalink to this definition">¶</a></dt>
<dd><p>how far any atom can move in a single line search in any dimension</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Minimization.etol">
<code class="descname">etol</code><a class="headerlink" href="#pysimm.lmps.Minimization.etol" title="Permalink to this definition">¶</a></dt>
<dd><p>energy tolerance default=1e-3</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Minimization.ftol">
<code class="descname">ftol</code><a class="headerlink" href="#pysimm.lmps.Minimization.ftol" title="Permalink to this definition">¶</a></dt>
<dd><p>force tolerance default=1e-3</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Minimization.maxiter">
<code class="descname">maxiter</code><a class="headerlink" href="#pysimm.lmps.Minimization.maxiter" title="Permalink to this definition">¶</a></dt>
<dd><p>maximum iterations default=10000</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">max eval</code></dt>
<dd><p>maximum force evaluations default=100000</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Minimization.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Minimization.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Minimization.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Create LAMMPS input for an energy minimization simulation.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Simulation" title="pysimm.lmps.Simulation"><code class="xref py py-class docutils literal"><span class="pre">Simulation</span></code></a> object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">input string</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.MolecularDynamics">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">MolecularDynamics</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#MolecularDynamics"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.MolecularDynamics" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Template object to contain LAMMPS MD settings</p>
<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.name">
<code class="descname">name</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.name" title="Permalink to this definition">¶</a></dt>
<dd><p>name to identify MD</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.group">
<code class="descname">group</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.group" title="Permalink to this definition">¶</a></dt>
<dd><p><a class="reference internal" href="#pysimm.lmps.Group" title="pysimm.lmps.Group"><code class="xref py py-class docutils literal"><span class="pre">Group</span></code></a> object for integrator</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.timestep">
<code class="descname">timestep</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.timestep" title="Permalink to this definition">¶</a></dt>
<dd><p>timestep value to use during MD</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.ensemble">
<code class="descname">ensemble</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.ensemble" title="Permalink to this definition">¶</a></dt>
<dd><p>&#8216;nvt&#8217; or &#8216;npt&#8217; or &#8216;nve&#8217;; default=nve</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.limit">
<code class="descname">limit</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.limit" title="Permalink to this definition">¶</a></dt>
<dd><p>numerical value to use with nve when limiting particle displacement</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.temperature">
<code class="descname">temperature</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.temperature" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of settings for temperature (start, stop, damp)</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.pressure">
<code class="descname">pressure</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.pressure" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of settings for pressure (start, stop, damp)</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.run">
<code class="descname">run</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.run" title="Permalink to this definition">¶</a></dt>
<dd><p>length of MD simulation in number of timesteps or False to omit run command</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.unfix">
<code class="descname">unfix</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.unfix" title="Permalink to this definition">¶</a></dt>
<dd><p>True to include command to unfix integrator after run</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.rigid">
<code class="descname">rigid</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.rigid" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of settings for a rigid simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.MolecularDynamics.extra_keywords">
<code class="descname">extra_keywords</code><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.extra_keywords" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of extra keywords to append at the end of the LAMMPS fix integrator</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.MolecularDynamics.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#MolecularDynamics.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.MolecularDynamics.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Create LAMMPS input for a molecular dynamics simulation.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; pysimm.lmps.Simulation object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">input string</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.OutputSettings">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">OutputSettings</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#OutputSettings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.OutputSettings" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Template object to define thermo and dump output settings in a LAMMPS simulation. See LAMMPS documentation for further information</p>
<dl class="attribute">
<dt id="pysimm.lmps.OutputSettings.thermo">
<code class="descname">thermo</code><a class="headerlink" href="#pysimm.lmps.OutputSettings.thermo" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of settings for thermo output</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.OutputSettings.dump">
<code class="descname">dump</code><a class="headerlink" href="#pysimm.lmps.OutputSettings.dump" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of settings for dump output</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.OutputSettings.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#OutputSettings.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.OutputSettings.write" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Qeq">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Qeq</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Qeq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Qeq" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>pysimm.lmps.MolecularDynamics</p>
<p>Template object to contain LAMMPS qeq settings</p>
<dl class="attribute">
<dt id="pysimm.lmps.Qeq.cutoff">
<code class="descname">cutoff</code><a class="headerlink" href="#pysimm.lmps.Qeq.cutoff" title="Permalink to this definition">¶</a></dt>
<dd><p>distance cutoff for charge equilibration</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Qeq.tol">
<code class="descname">tol</code><a class="headerlink" href="#pysimm.lmps.Qeq.tol" title="Permalink to this definition">¶</a></dt>
<dd><p>tolerance (precision) for charge equilibration</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Qeq.max_iter">
<code class="descname">max_iter</code><a class="headerlink" href="#pysimm.lmps.Qeq.max_iter" title="Permalink to this definition">¶</a></dt>
<dd><p>maximum iterations</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Qeq.qfile">
<code class="descname">qfile</code><a class="headerlink" href="#pysimm.lmps.Qeq.qfile" title="Permalink to this definition">¶</a></dt>
<dd><p>file with qeq parameters (leave undefined for defaults)</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Qeq.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Qeq.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Qeq.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Create LAMMPS input for a charge equilibration calculation</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Simulation" title="pysimm.lmps.Simulation"><code class="xref py py-class docutils literal"><span class="pre">Simulation</span></code></a> object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">input string</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Region">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Region</code><span class="sig-paren">(</span><em>name='all'</em>, <em>style='block'</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Region"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Region" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pysimm.utils.html#pysimm.utils.Item" title="pysimm.utils.Item"><code class="xref py py-class docutils literal"><span class="pre">pysimm.utils.Item</span></code></a></p>
<p>Template object to create a region in a LAMMPS simulation. See LAMMPS documentation for further information</p>
<dl class="attribute">
<dt id="pysimm.lmps.Region.name">
<code class="descname">name</code><a class="headerlink" href="#pysimm.lmps.Region.name" title="Permalink to this definition">¶</a></dt>
<dd><p>name id for region</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Region.style">
<code class="descname">style</code><a class="headerlink" href="#pysimm.lmps.Region.style" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS region style</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">*args</code></dt>
<dd><p>args for given style</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">**kwargs</code></dt>
<dd><p>optional kwargs for region command</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Region.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Region.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Region.write" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Simulation">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Simulation</code><span class="sig-paren">(</span><em>s</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
<p>Organizational object for LAMMPS simulation. Should contain combination of
<a class="reference internal" href="#pysimm.lmps.MolecularDynamics" title="pysimm.lmps.MolecularDynamics"><code class="xref py py-class docutils literal"><span class="pre">MolecularDynamics</span></code></a>, <a class="reference internal" href="#pysimm.lmps.Minimization" title="pysimm.lmps.Minimization"><code class="xref py py-class docutils literal"><span class="pre">Minimization</span></code></a>, and/or <a class="reference internal" href="#pysimm.lmps.CustomInput" title="pysimm.lmps.CustomInput"><code class="xref py py-class docutils literal"><span class="pre">CustomInput</span></code></a> object.</p>
<dl class="attribute">
<dt id="pysimm.lmps.Simulation.forcefield">
<code class="descname">forcefield</code><a class="headerlink" href="#pysimm.lmps.Simulation.forcefield" title="Permalink to this definition">¶</a></dt>
<dd><p>name of force field for simulation settings</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.name">
<code class="descname">name</code><a class="headerlink" href="#pysimm.lmps.Simulation.name" title="Permalink to this definition">¶</a></dt>
<dd><p>name for simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.log">
<code class="descname">log</code><a class="headerlink" href="#pysimm.lmps.Simulation.log" title="Permalink to this definition">¶</a></dt>
<dd><p>LAMMPS log filename</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.write">
<code class="descname">write</code><a class="headerlink" href="#pysimm.lmps.Simulation.write" title="Permalink to this definition">¶</a></dt>
<dd><p>file name to write final LAMMPS data file default=None</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.print_to_screen">
<code class="descname">print_to_screen</code><a class="headerlink" href="#pysimm.lmps.Simulation.print_to_screen" title="Permalink to this definition">¶</a></dt>
<dd><p>True to have LAMMPS output printed to stdout after simulation ends</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.debug">
<code class="descname">debug</code><a class="headerlink" href="#pysimm.lmps.Simulation.debug" title="Permalink to this definition">¶</a></dt>
<dd><p>True to have LAMMPS output streamed to stdout during simulation (WARNING: this may degrade performance)</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.custom">
<code class="descname">custom</code><a class="headerlink" href="#pysimm.lmps.Simulation.custom" title="Permalink to this definition">¶</a></dt>
<dd><p>option to flag simulation as purley custom input to skip prepaing initialization</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.add">
<code class="descname">add</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.add"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.add" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.add_custom">
<code class="descname">add_custom</code><span class="sig-paren">(</span><em>custom=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.add_custom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.add_custom" title="Permalink to this definition">¶</a></dt>
<dd><p>Add custom input string to simulation</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>custom</strong> &#8211; custom LAMMPS input string to add to Simulation</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.add_md">
<code class="descname">add_md</code><span class="sig-paren">(</span><em>template=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.add_md"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.add_md" title="Permalink to this definition">¶</a></dt>
<dd><p>Add <code class="xref py py-class docutils literal"><span class="pre">MolecularDyanmics</span></code> template to simulation</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>template</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.MolecularDynamics" title="pysimm.lmps.MolecularDynamics"><code class="xref py py-class docutils literal"><span class="pre">MolecularDynamics</span></code></a> object reference</li>
<li><strong>**kwargs</strong> &#8211; if template is None these are passed to <a class="reference internal" href="#pysimm.lmps.MolecularDynamics" title="pysimm.lmps.MolecularDynamics"><code class="xref py py-class docutils literal"><span class="pre">MolecularDynamics</span></code></a> constructor to create new template</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.add_min">
<code class="descname">add_min</code><span class="sig-paren">(</span><em>template=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.add_min"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.add_min" title="Permalink to this definition">¶</a></dt>
<dd><p>Add <a class="reference internal" href="#pysimm.lmps.Minimization" title="pysimm.lmps.Minimization"><code class="xref py py-class docutils literal"><span class="pre">Minimization</span></code></a> template to simulation</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>template</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Minimization" title="pysimm.lmps.Minimization"><code class="xref py py-class docutils literal"><span class="pre">Minimization</span></code></a> object reference</li>
<li><strong>**kwargs</strong> &#8211; if template is None these are passed to <a class="reference internal" href="#pysimm.lmps.Minimization" title="pysimm.lmps.Minimization"><code class="xref py py-class docutils literal"><span class="pre">Minimization</span></code></a> constructor to create new template</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.add_qeq">
<code class="descname">add_qeq</code><span class="sig-paren">(</span><em>template=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.add_qeq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.add_qeq" title="Permalink to this definition">¶</a></dt>
<dd><p>Add <a class="reference internal" href="#pysimm.lmps.Qeq" title="pysimm.lmps.Qeq"><code class="xref py py-class docutils literal"><span class="pre">Qeq</span></code></a> template to simulation</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>template</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Qeq" title="pysimm.lmps.Qeq"><code class="xref py py-class docutils literal"><span class="pre">Qeq</span></code></a> object reference</li>
<li><strong>**kwargs</strong> &#8211; if template is None these are passed to <a class="reference internal" href="#pysimm.lmps.Qeq" title="pysimm.lmps.Qeq"><code class="xref py py-class docutils literal"><span class="pre">Qeq</span></code></a> constructor to create new template</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Simulation.input">
<code class="descname">input</code><a class="headerlink" href="#pysimm.lmps.Simulation.input" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.run">
<code class="descname">run</code><span class="sig-paren">(</span><em>np=None</em>, <em>nanohub=None</em>, <em>save_input=True</em>, <em>prefix='mpiexec'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.run" title="Permalink to this definition">¶</a></dt>
<dd><p>Begin LAMMPS simulation.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>np</strong> &#8211; number of threads to use (serial by default) default=None</li>
<li><strong>nanohub</strong> &#8211; dictionary containing nanohub resource information default=None</li>
<li><strong>init</strong> &#8211; True to write initialization part of LAMMPS input script (set to False if using complete custom input)</li>
<li><strong>save_input</strong> &#8211; True to save input as pysimm.sim.in</li>
<li><strong>prefix</strong> &#8211; prefix for running LAMMPS (i.e. - mpiexec)</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Simulation.write_input">
<code class="descname">write_input</code><span class="sig-paren">(</span><em>init=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Simulation.write_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Simulation.write_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates LAMMPS input string including initialization and input from templates/custom input</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>None</strong> &#8211; </td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.SteeredMolecularDynamics">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">SteeredMolecularDynamics</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#SteeredMolecularDynamics"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.SteeredMolecularDynamics" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pysimm.lmps.MolecularDynamics" title="pysimm.lmps.MolecularDynamics"><code class="xref py py-class docutils literal"><span class="pre">pysimm.lmps.MolecularDynamics</span></code></a></p>
<dl class="method">
<dt id="pysimm.lmps.SteeredMolecularDynamics.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#SteeredMolecularDynamics.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.SteeredMolecularDynamics.write" title="Permalink to this definition">¶</a></dt>
<dd><p>Create LAMMPS input for a steered molecular dynamics simulation.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sim</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Simulation" title="pysimm.lmps.Simulation"><code class="xref py py-class docutils literal"><span class="pre">Simulation</span></code></a> object reference</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">input string</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="pysimm.lmps.Velocity">
<em class="property">class </em><code class="descclassname">pysimm.lmps.</code><code class="descname">Velocity</code><span class="sig-paren">(</span><em>group=&lt;pysimm.lmps.Group object&gt;</em>, <em>style='create'</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Velocity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Velocity" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pysimm.utils.html#pysimm.utils.Item" title="pysimm.utils.Item"><code class="xref py py-class docutils literal"><span class="pre">pysimm.utils.Item</span></code></a></p>
<p>Template object to define velocity initialization in a LAMMPS simulation. See LAMMPS documentation for further information</p>
<dl class="attribute">
<dt id="pysimm.lmps.Velocity.group">
<code class="descname">group</code><a class="headerlink" href="#pysimm.lmps.Velocity.group" title="Permalink to this definition">¶</a></dt>
<dd><p>group for velocity command</p>
</dd></dl>

<dl class="attribute">
<dt id="pysimm.lmps.Velocity.style">
<code class="descname">style</code><a class="headerlink" href="#pysimm.lmps.Velocity.style" title="Permalink to this definition">¶</a></dt>
<dd><p>style for the velocity command</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">*args</code></dt>
<dd><p>arguments for the given style</p>
</dd></dl>

<dl class="method">
<dt id="pysimm.lmps.Velocity.write">
<code class="descname">write</code><span class="sig-paren">(</span><em>sim=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#Velocity.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.Velocity.write" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.call_lammps">
<code class="descclassname">pysimm.lmps.</code><code class="descname">call_lammps</code><span class="sig-paren">(</span><em>simulation</em>, <em>np</em>, <em>nanohub</em>, <em>prefix='mpiexec'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#call_lammps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.call_lammps" title="Permalink to this definition">¶</a></dt>
<dd><p>Wrapper to call LAMMPS using executable name defined in pysimm.lmps module.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>simulation</strong> &#8211; <a class="reference internal" href="#pysimm.lmps.Simulation" title="pysimm.lmps.Simulation"><code class="xref py py-class docutils literal"><span class="pre">Simulation</span></code></a> object reference</li>
<li><strong>np</strong> &#8211; number of threads to use</li>
<li><strong>nanohub</strong> &#8211; dictionary containing nanohub resource information default=None</li>
<li><strong>prefix</strong> &#8211; prefix for running LAMMPS (i.e. - mpiexec)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.check_lmps_attr">
<code class="descclassname">pysimm.lmps.</code><code class="descname">check_lmps_attr</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#check_lmps_attr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.check_lmps_attr" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="function">
<dt id="pysimm.lmps.check_lmps_exec">
<code class="descclassname">pysimm.lmps.</code><code class="descname">check_lmps_exec</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#check_lmps_exec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.check_lmps_exec" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="function">
<dt id="pysimm.lmps.energy">
<code class="descclassname">pysimm.lmps.</code><code class="descname">energy</code><span class="sig-paren">(</span><em>s</em>, <em>all=False</em>, <em>np=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#energy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.energy" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience function to calculate energy of a given <a class="reference internal" href="pysimm.system.html#pysimm.system.System" title="pysimm.system.System"><code class="xref py py-class docutils literal"><span class="pre">System</span></code></a> object.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; system to calculate energy</li>
<li><strong>all</strong> &#8211; returns decomposition of energy if True (default: False)</li>
<li><strong>np</strong> &#8211; number of threads to use for simulation</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">total energy or disctionary of energy components</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.enqueue_output">
<code class="descclassname">pysimm.lmps.</code><code class="descname">enqueue_output</code><span class="sig-paren">(</span><em>out</em>, <em>queue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#enqueue_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.enqueue_output" title="Permalink to this definition">¶</a></dt>
<dd><p>Helps queue output for printing to screen during simulation.</p>
</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.qeq">
<code class="descclassname">pysimm.lmps.</code><code class="descname">qeq</code><span class="sig-paren">(</span><em>s</em>, <em>np=None</em>, <em>nanohub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#qeq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.qeq" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience function to call a qeq calculation. kwargs are passed to <a class="reference internal" href="#pysimm.lmps.Qeq" title="pysimm.lmps.Qeq"><code class="xref py py-class docutils literal"><span class="pre">Qeq</span></code></a> constructor</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; system to perform simulation on</li>
<li><strong>np</strong> &#8211; number of threads to use</li>
<li><strong>nanohub</strong> &#8211; dictionary containing nanohub resource information default=None</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.quick_md">
<code class="descclassname">pysimm.lmps.</code><code class="descname">quick_md</code><span class="sig-paren">(</span><em>s</em>, <em>np=None</em>, <em>nanohub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#quick_md"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.quick_md" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience function to call an individual MD simulation. kwargs are passed to MD constructor</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; system to perform simulation on</li>
<li><strong>np</strong> &#8211; number of threads to use</li>
<li><strong>nanohub</strong> &#8211; dictionary containing nanohub resource information default=None</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.lmps.quick_min">
<code class="descclassname">pysimm.lmps.</code><code class="descname">quick_min</code><span class="sig-paren">(</span><em>s</em>, <em>np=None</em>, <em>nanohub=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/lmps.html#quick_min"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.lmps.quick_min" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience function to call an individual energy minimization simulation. kwargs are passed to min constructor</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; system to perform simulation on</li>
<li><strong>np</strong> &#8211; number of threads to use</li>
<li><strong>nanohub</strong> &#8211; dictionary containing nanohub resource information default=None</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

</div>


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